texshade: useful, and still kickin’

I’ve been looking at doing an analysis with some protein subfamily sequence logos, using Eric Beitz’s texshade. While it’s a little strange that it does the actual analysis part (rather than just the rendering) using LaTeX, it’s the only implementation of the method I know of, and it beats reimplementing it from the paper.

Although it was published in 2006 (and earlier in 2000), with the original URLs now dead, I noticed the latest update for the version of texshade in CTAN (v1.18) was on 15th of April, 2008 … ie texshade was updated just 14 days ago !

It happens all to often that published bioinformatics tools cease to be updated or even disappear from the Web not long after the peer-review publication is released. Kudos to Eric for not abandoning his software.

2 thoughts on “texshade: useful, and still kickin’

  1. Thanks for bringing Texshade to my attention – I never heard of this program before. Texshade seems to have a number of advantages over Boxshade (from which it has borrowed several ideas), one of them being that Texshade is still actively maintained while Boxshade has been mothballed 12 years ago.
    BTW, the paper does not say that Texshade can do sequence logos – is this some more recent developments?

  2. Glad to be of assistance 🙂
    So there are two papers, the 2006 one and the 2000 one. It’s the 2006 paper that talks about the sequence logo features. Despite this, the best and most up-to-date texshade reference is probably the pdf manual that comes with the package on CTAN.

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